Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes.
Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes.
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DOI：
10.1093/dnares/dsr010
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发表时间：
2011-06
期刊：
影响因子：
--
通讯作者：
Saitou N
中科院分区：
文献类型：
--
作者：
Suzuki R;Saitou N
蛋白质编码基因的主要作用是编码氨基酸。因此，不改变编码氨基酸的密码子同义位点被认为是中性进化的。然而，如果蛋白质编码基因的某个区域含有功能性核苷酸元件（例如剪接信号），则该区域中的同义位点可能具有选择压力。这些元件的存在将通过搜索低核苷酸取代的区域来检测。我们对6种哺乳动物（智人、猕猴、小家鼠、褐家鼠、牛和家犬）的10 790个同源基因的保守性核苷酸序列进行了分析，提取了4150个保守性明显强于其他区域的序列，并将其命名为显著保守编码序列（SCCSs）。在2273个基因中观察到SCCS。这些基因主要与发育、转录调控和神经元有关，并在神经系统和头颈部器官中表达。在SCCSs中没有观察到影响同义替换的常规因素的强烈影响。这些结果表明，SCCS可能具有核苷酸元件和蛋白质编码序列的双重功能，并保留在哺乳动物的进化过程中。
The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10 790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.
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